scFEA: A graph neural network model to estimate cell-wise metabolic using single cell RNA-seq data

github链接GitHub - changwn/scFEA: single cell Flux Estimation Analysis (scFEA) Try the below web server!

Package Tutorial

seurat对象使用scFEAscFEA/scFEA_tutorial2.ipynb at master · changwn/scFEA · GitHub

1.创建新环境python310

conda create -n python310 python=3.10

2.进入新环境python310

conda activate python310

3.下载scFEA

cd scFEA
conda install --file requirements
conda install pytorch torchvision -c pytorch
pip install --user magic-impute

4.检查scFEA是否安装好

python src/scFEA.py --help

5.尝试运行代码，一直出问题，append的问题

FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.

重装了pandas

并将scFEA.py文件第172行改为geneExprDf = pd.concat([geneExprDf, temp], ignore_index=True)

才可以运行